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helena-bioinformatics

Noodle Biomedical Literature Discovery MCP

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Explore a PMID literature neighborhood

get_publication_neighborhood
Read-onlyIdempotent

Retrieve the citation and semantic neighborhood around a single PubMed ID to uncover related biomedical publications for literature discovery and professional review.

Instructions

Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidYesOne PubMed identifier, as 1 to 12 digits.
from_work_idNoOptional prior work ID for a reversible graph path.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
edgesYes
nodesYes
freshnessYes
anchor_pmidNo
stale_afterYes
generated_atYes
graph_versionYes
anchor_node_idYes
anchor_work_idNo
policy_versionYes
usage_boundaryYes
release_channelYes
contract_versionYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint=false, so the description does not need to restate safety. It adds useful behavioral context: the neighborhood is 'bounded', and results are intended for discovery/review rather than clinical decisions. No contradiction with annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two short sentences with no filler. The main action is front-loaded, and the purpose/limitation sentence earns its place by clarifying the appropriate use context.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a read-only, two-parameter tool with a full input schema and an output schema, the description is sufficient. It conveys the essential scope ('bounded neighborhood'), the intended use, and the non-clinical boundary. Missing sibling routing is a minor gap rather than a completeness failure.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents pmid and from_work_id, including the pattern, optionality, default, and 'reversible graph path' semantics. The description adds no additional parameter detail beyond restating that the operation centers on one PMID.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb ('Retrieve'), a specific resource ('bounded citation and semantic neighborhood'), and a precise identifier ('one PMID'). The name and description together clearly distinguish this from sibling tools like get_work_neighborhood (work ID) and get_publication_details (details, not neighborhood).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies the tool is for literature discovery and explicitly rules out diagnosis/treatment, but it does not name sibling alternatives or state when to choose this tool over get_work_neighborhood or get_publication_details. The primary usage context is clear, yet routing guidance is left to inference.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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